[R] Warning messages while parallel computing

[Henrik Bengtsson]

I don't think 'parallel' is to blame in this case. Those warnings:

Warning in for (i in seq_len(Ne + echo)) { :
  closing unused connection 19

come from base::source()
[https://github.com/wch/r-source/blob/9caddc1eaad1f480283f1e98af34a328699d1869/src/library/base/R/source.R#L166-L244].

Unless there's a bug in source() that leaves connections open, which
is unlikely, I think there's something in the 'xx.R' script that opens
a connection but doesn't close it.  Possibly multiple times.  A good
check is to see if the same warnings are produced when calling
source("xx.R") sequentially in a for() loop or an lapply() call.

Hope this helps,

Henrik

On Thu, Mar 4, 2021 at 9:58 AM Bill Dunlap <williamwdunlap using gmail.com> wrote:
>
> To avoid the warnings from gc(), call parallel::stopCluster(cl) before
> removing or overwriting cl.
>
> -Bill
>
> On Thu, Mar 4, 2021 at 1:52 AM Shah Alam <dr.alamsolangi using gmail.com> wrote:
> >
> > Hello everyone,
> >
> > I am using the "parallel" R package for parallel computation.
> >
> > Code:
> >
> >    # set number of cores
> >     cl <- makeCluster(8, type = "PSOCK")  # Mac/Linux need to set as "FORK"
> >
> >       # pass functions and objects to the cluster environment and set seed
> >       # all the items exported need to stay in the global environment!!
> >       clusterCall(cl, function() { source("xx.R" )})
> >       clusterExport(cl, list("a", "b", "c", "d",
> >                              "5"))
> >       clusterSetRNGStream(cl, 1)
> >
> > While parallel processing, I receive the following warning signs.  Do I
> > need to ignore these signs or do they potentially slow the whole process?
> >
> >  *  Warning signs:*
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 19
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 18
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 17
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 16
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 15
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 14
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 13
> > Warning in for (i in seq_len(Ne + echo)) { :
> >   closing unused connection 12
> >
> > Best regards,
> > Shah Alam
> >
> >         [[alternative HTML version deleted]]
> >
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